Summary: Mapping ancient DNA to a reference genome is challenging as it involves numerous steps, is time-consuming and has to be repeated within a study to assess the quality of extracts and libraries; as a result, the mapping needs to be automatized to handle large amounts of data in a reproducible way. We present mapache, a flexible, robust, and scalable pipeline to map, quantify and impute ancient and present-day DNA in a reproducible way. Mapache is implemented in the workflow manager Snakemake and is optimized for low-space consumption, allowing to efficiently (re)map large data sets such as reference panels and multiple extracts and libraries.
@article{arxiv.2208.13283,
title = {Mapache: a flexible pipeline to map ancient DNA},
author = {Samuel Neuenschwander and Diana I. Cruz Dávalos and Lucas Anchieri and Bárbara Sousa da Mota and Davide Bozzi and Simone Rubinacci and Olivier Delaneau and Simon Rasmussen and Anna-Sapfo Malaspinas},
journal= {arXiv preprint arXiv:2208.13283},
year = {2023}
}
Comments
Availability: Mapache is freely available on GitHub (https://github.com/sneuensc/mapache). Supplementary information: An extensive manual is provided at https://github.com/sneuensc/mapache/wiki